Aim

pMT06 was transfected into various cell types and mRNA barcode counts were sequenced together with pMT06 pDNA counts. In four different sequencing runs, data for all P53 & GR reporters was collected, and will be analyzed here.

Setup

Libraries

Functions

Loading data

Creating count data frames

Read distribution

Read distribution per cutoff

pDNA-cDNA correlation

Replicate correlation

Stuff learned from above figures:
Some samples can be excluded from further analysis because they don’t contain useful information, these samples are:
MCF7-KO-DMSO: rep2_seq1, rep1_seq1(?), r2_seq2(?), r1_seq3, r3_seq3
MCF7-KO-Nutlin: rep2_seq1, rep3_seq1(?), r1_seq2, r1_seq3, r3_seq3
MCF7-WT-DMSO: rep2_seq1, rep3_seq1
MCF7-WT-Nutlin: rep3_seq1, r2_seq2, r1_seq3
A549_DMSO: r2_seq3, r3_seq3
A549_Dex10: r2_seq3
A549_Dex100: r2_seq3
A549-Dex-1: r1_seq2, r2_seq3
mES-N2B27-HQ: rep1_seq1
mES-N2B27-RA: rep1_seq1, rep2_seq1

Normalization of barcode counts:

Divide cDNA barcode counts through pDNA barcode counts

Characterize reporter activities

Reporter activity correlations

Removing outliers

Annotation

Technical replicate correlations

Export data

Session Info

paste("Run time: ",format(Sys.time()-StartTime))
## [1] "Run time:  8.081767 mins"
getwd()
## [1] "/DATA/usr/m.trauernicht/projects/SuRE_deep_scan_trp53_gr/analyses"
date()
## [1] "Thu Jul  1 15:04:51 2021"
sessionInfo()
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] tidyr_1.1.3          viridis_0.6.0        viridisLite_0.4.0   
##  [4] ggpointdensity_0.1.0 ggbiplot_0.55        scales_1.1.1        
##  [7] factoextra_1.0.7     shiny_1.6.0          pheatmap_1.0.12     
## [10] gridExtra_2.3        RColorBrewer_1.1-2   readr_1.4.0         
## [13] haven_2.4.1          ggbeeswarm_0.6.0     plotly_4.9.3        
## [16] tibble_3.1.1         dplyr_1.0.5          vwr_0.3.0           
## [19] latticeExtra_0.6-29  lattice_0.20-41      stringdist_0.9.6.3  
## [22] GGally_2.1.1         ggpubr_0.4.0         ggplot2_3.3.3       
## [25] stringr_1.4.0        plyr_1.8.6           data.table_1.14.0   
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.2        tools_4.0.5       backports_1.2.1   bslib_0.2.4      
##  [5] utf8_1.2.1        R6_2.5.0          vipor_0.4.5       DBI_1.1.1        
##  [9] lazyeval_0.2.2    colorspace_2.0-0  withr_2.4.2       tidyselect_1.1.1 
## [13] curl_4.3          compiler_4.0.5    labeling_0.4.2    sass_0.3.1       
## [17] digest_0.6.27     foreign_0.8-81    rmarkdown_2.7     rio_0.5.26       
## [21] jpeg_0.1-8.1      pkgconfig_2.0.3   htmltools_0.5.1.1 highr_0.9        
## [25] fastmap_1.1.0     htmlwidgets_1.5.3 rlang_0.4.10      readxl_1.3.1     
## [29] farver_2.1.0      jquerylib_0.1.4   generics_0.1.0    jsonlite_1.7.2   
## [33] crosstalk_1.1.1   zip_2.1.1         car_3.0-10        magrittr_2.0.1   
## [37] Rcpp_1.0.6        munsell_0.5.0     fansi_0.4.2       abind_1.4-5      
## [41] lifecycle_1.0.0   stringi_1.5.3     yaml_2.2.1        carData_3.0-4    
## [45] promises_1.2.0.1  ggrepel_0.9.1     forcats_0.5.1     crayon_1.4.1     
## [49] hms_1.0.0         knitr_1.33        pillar_1.6.0      ggsignif_0.6.1   
## [53] reshape2_1.4.4    glue_1.4.2        evaluate_0.14     png_0.1-7        
## [57] vctrs_0.3.8       httpuv_1.6.0      cellranger_1.1.0  gtable_0.3.0     
## [61] purrr_0.3.4       reshape_0.8.8     assertthat_0.2.1  xfun_0.22        
## [65] openxlsx_4.2.3    mime_0.10         xtable_1.8-4      broom_0.7.6      
## [69] rstatix_0.7.0     later_1.2.0       beeswarm_0.3.1    ellipsis_0.3.2